Literature DB >> 23648627

In vitro regulatory models for systems biology.

Anthony J Genot1, Teruo Fujii, Yannick Rondelez.   

Abstract

The reductionist approach has revolutionized biology in the past 50 years. Yet its limits are being felt as the complexity of cellular interactions is gradually revealed by high-throughput technology. In order to make sense of the deluge of "omic data", a hypothesis-driven view is needed to understand how biomolecular interactions shape cellular networks. We review recent efforts aimed at building in vitro biochemical networks that reproduce the flow of genetic regulation. We highlight how those efforts have culminated in the rational construction of biochemical oscillators and bistable memories in test tubes. We also recapitulate the lessons learned about in vivo biochemical circuits such as the importance of delays and competition, the links between topology and kinetics, as well as the intriguing resemblance between cellular reaction networks and ecosystems.
Copyright © 2013 Elsevier Inc. All rights reserved.

Keywords:  DNA nanotechnology; Dynamical systems; Genetic regulation; Molecular programming; Reaction network; Systems biology

Mesh:

Year:  2013        PMID: 23648627     DOI: 10.1016/j.biotechadv.2013.04.008

Source DB:  PubMed          Journal:  Biotechnol Adv        ISSN: 0734-9750            Impact factor:   14.227


  4 in total

1.  Rapid cell-free forward engineering of novel genetic ring oscillators.

Authors:  Henrike Niederholtmeyer; Zachary Z Sun; Yutaka Hori; Enoch Yeung; Amanda Verpoorte; Richard M Murray; Sebastian J Maerkl
Journal:  Elife       Date:  2015-10-05       Impact factor: 8.140

2.  Boosting functionality of synthetic DNA circuits with tailored deactivation.

Authors:  Kevin Montagne; Guillaume Gines; Teruo Fujii; Yannick Rondelez
Journal:  Nat Commun       Date:  2016-11-15       Impact factor: 14.919

3.  Cascaded dissipative DNAzyme-driven layered networks guide transient replication of coded-strands as gene models.

Authors:  Jianbang Wang; Zhenzhen Li; Itamar Willner
Journal:  Nat Commun       Date:  2022-07-29       Impact factor: 17.694

4.  A small-molecule chemical interface for molecular programs.

Authors:  Vasily A Shenshin; Camille Lescanne; Guillaume Gines; Yannick Rondelez
Journal:  Nucleic Acids Res       Date:  2021-07-21       Impact factor: 16.971

  4 in total

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